Effect of ligand structure in the trimethylene carbonate polymerization by cationic zirconocene catalysts: A “naked model” DFT study

Mechanism of cationic ring-opening polymerisation of ε-caprolactone using metallocene/borate catalytic systems: a DFT and NCI study on chain initiation, propagation and termination

We present a comprehensive DFT investigation on the cationic ring-opening polymerisation (CROP) of ε-caprolactone (CL) using zirconocene/borate catalyst systems. All possible pathways of the interaction between cationic species [Cp2ZrMe+] and counteranions, [A-] = [MeB(C6F5)3]- and [B(C6F5)4]-, were examined during chain initiation, propagation, and termination steps. The calculations reveal an active chain-end mechanism with O-alkyl bond cleavage of the polymerisation. The catalytic performance of the two counteranions is found to be identical, and they influence the initial process through stabilisation of the cationic species via non-covalent interactions (NCI), with the [MeB(C6F5)3]- anion stabilising the catalyst-monomer complex more effectively than the [B(C6F5)4]- anion by 24.3 kJ mol-1. The first two propagations are likely the rate-determining step, with calculated free-energy barriers of 61.4-71.2 and 73.9-80.6 kJ mol-1 with and without the anions (A-), respectively. The presence of the counteranion significantly affects the third propagation rate, lowering the barriers up to 20 kJ mol-1. Comparison of the first termination and the third propagation shows that they are not competitive, with the termination being less facile. We also studied the initiation and propagation steps for the hafnocene catalyst and found that the Hf catalyst slightly favours the CL CROP in comparison to the Zr catalyst. Analysis of solvent and dispersion interaction demonstrates that both factors play an important role in the process. NCI analysis reveals weak (van der Waals) interactions at the contacts between the cationic species and the counteranions during the reaction course. Overall, our results offer insights into the structures and interactions involved in the polymerisation.

Computational evaluation of zirconocene catalysts for ε-caprolactone cationic ring-opening polymerization

This quantum chemical study presents the ligand effect and a structure-property relationship in the cationic ring-opening polymerization (CROP) of ε-caprolactone using zirconocene catalysts. We first examined the effects of catalyst structure on the initiation and chain propagation steps of the CROP process. A total of 54 catalyst structures were investigated to understand the influence of the ligand structure on the stability of the catalyst-monomer complex and polymerization activity. The properties of the catalysts were analyzed in terms of ancillary ligands, ligand substituents, and bridging units. Calculations showed that the polymerization follows a proposed cationic mechanism, with ring opening occurring via alkyl-bond cleavage. A correlation between complex stability and activation energy was also observed, with ligand substituents dominating in both steps. While the ancillary ligands directly affect the HOMO energy level, the bridges are mainly responsible for the catalyst geometries, resulting in reduced complex stability and higher activation energy for the propagation step. This study contributes to a better understanding of the structural characteristics of zirconocene catalysts, which offers guidance for improving CROP activities in lactone polymerization.

Mechanism of Melatonin Metabolism by CYP1A1: What Determines the Bifurcation Pathways of Hydroxylation versus Deformylation?

Melatonin, a widely applied cosmetic active ingredient, has a variety of uses as a skin protector through antioxidant and anti-inflammatory functions as well as giving the body UV-induced defenses and immune system support. In the body, melatonin is synthesized from a tryptophan amino acid in a cascade of reactions, but as melatonin is toxic at high concentrations, it is metabolized in the human skin by the cytochrome P450 enzymes. The P450s are diverse heme-based mono-oxygenases that catalyze oxygen atom-transfer processes that trigger metabolism and detoxification reactions in the body. In the catalytic cycle of the P450s, a short-lived high-valent iron(IV)-oxo heme cation radical is formed that has been proposed to be the active oxidant. How and why it activates melatonin in the human body and what the origin of the product distributions is, are unknown. This encouraged us to do a detailed computational study on a typical human P450 isozyme, namely CYP1A1. We initially did a series of molecular dynamics simulations with substrate docked into several orientations. These simulations reveal a number of stable substrate-bound positions in the active site, which may lead to differences in substrate activation channels. Using tunneling analysis on the full protein structures, we show that two of the four binding conformations lead to open substrate-binding pockets. As a result, in these open pockets, the substrate is not tightly bound and can escape back into the solution. In the closed conformations, in contrast, the substrate is mainly oriented with the methoxy group pointing toward the heme, although under a different angle. We then created large quantum cluster models of the enzyme and focused on the chemical reaction mechanisms for melatonin activation, leading to competitive O-demethylation and C⁶-aromatic hydroxylation pathways. The calculations show that active site positioning determines the product distributions, but the bond that is activated is not necessarily closest to the heme in the enzyme-substrate complex. As such, the docking and molecular dynamics positioning of the substrate versus oxidant can give misleading predictions on product distributions. In particular, in quantum mechanics cluster model I, we observe that through a tight hydrogen bonding network, a preferential 6-hydroxylation of melatonin is obtained. However, O-demethylation becomes possible in alternative substrate-binding orientations that have the C⁶-aromatic ring position shielded. Finally, we investigated enzymatic and non-enzymatic O-demethylation processes and show that the hydrogen bonding network in the substrate-binding pocket can assist and perform this step prior to product release from the enzyme.

DFT Investigations on the Ring-Opening Polymerization of Trimethylene Carbonate Catalysed by Heterocyclic Nitrogen Bases

Organocatalysts for polymerization have known a huge interest over the last two decades. Among them, heterocyclic nitrogen bases are widely used to catalyse the ring-opening polymerization (ROP) of heterocycles such as cyclic carbonates. We have investigated the ring-opening polymerization of trimethylene carbonate (TMC) catalysed by DMAP (4-dimethylaminopyridine) and TBD (1,5,7-triazabicyclo[4.4.0]dec-5-ene) as case studies in the presence of methanol as co-initiator by Density Functional Theory (DFT). A dual mechanism based on H-bond activation of the carbonyl moieties of the monomer and a basic activation of the alcohol co-initiator has been shown to occur more preferentially than a direct nucleophilic attack of the carbonate monomer by the heterocyclic nitrogen catalyst. The rate-determining step of the mechanism is the ring opening of the TMC molecule, which is slightly higher than the nucleophilic attack of the TMC carbonyl by the activated alcohol. The calculations also indicate TBD as a more efficient catalyst than DMAP. The higher energy barrier found for DMAP vs. TBD, 23.7 vs. 11.3 kcal·mol−1, is corroborated experimentally showing a higher reactivity for the latter.

Coordination Ring-Opening Polymerization of Cyclic Esters: A Critical Overview of DFT Modeling and Visualization of the Reaction Mechanisms

Ring-opening polymerization (ROP) of cyclic esters (lactones, lactides, cyclic carbonates and phosphates) is an effective tool to synthesize biocompatible and biodegradable polymers. Metal complexes effectively catalyze ROP, a remarkable diversity of the ROP mechanisms prompted the use of density functional theory (DFT) methods for simulation and visualization of the ROP pathways. Optimization of the molecular structures of the key reaction intermediates and transition states has allowed to explain the values of catalytic activities and stereocontrol events. DFT computation data sets might be viewed as a sound basis for the design of novel ROP catalysts and cyclic substrates, for the creation of new types of homo- and copolymers with promising properties. In this review, we summarized the results of DFT modeling of coordination ROP of cyclic esters. The importance to understand the difference between initiation and propagation stages, to consider the possibility of polymer-catalyst coordination, to figure out the key transition states, and other aspects of DFT simulation and visualization of ROP have been also discussed in our review.

Data on electronic structures for the study of ligand effects on the zirconocene-mediated trimethylene carbonate polymerization

The data presented in this paper are related to the research article entitled “Effect of ligand structure in the trimethylene carbonate polymerization by cationic zirconocene catalysts: A “naked model” DFT study” (Jitonnom and Meelua, 2017) [1]. In this data article, we present 3D molecular information of 29 zirconocene catalysts that differ in electronic and steric properties. The data contains all cationic species along the initiation and first propagation step of the polymerization, which are provided in a PDB format that can be used for further studies.